Pajari topped an all-Ford Fiesta Rally3 leaderboard after winning all eight treacherous stages with co-driver Enni Mälkönen.
The 20-year-old Finn had no issues to report as he arrived back in Zagreb 14min 17.8sec ahead of nearest challenger Zoltán László.
"I had a lack of confidence in the morning," explained Pajari. "There were so many muddy places and I just didn't feel too confident.
"I was avoiding the biggest cuts and we didn't have any punctures, so it was actually not bad. We need to continue the same way," he added.
Home hero Ivica Siladic was 1min 31.2sec behind László in third, with experienced Italian Enrico Brazzoli 1min 31.2sec further back. Asphalt debutant Mcrae Kimathi completed the leaderboard.
William Creighton was the only casualty of the day. The Irishman retired on the second stage after going off the road and damaging the rear axle of his Fiesta.
• Full coverage from the Croatia Rally will be available on WRC+ All Live here, including every stage broadcast as it happens as well as key interviews, features and expert analysis from the service park
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